lindenb / jvarkitLinks
Java utilities for Bioinformatics
☆510Updated 2 weeks ago
Alternatives and similar repositories for jvarkit
Users that are interested in jvarkit are comparing it to the libraries listed below
Sorting:
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆488Updated 2 months ago
- Graph-based alignment (Hierarchical Graph FM index)☆514Updated last month
- Transcript assembly and quantification for RNA-Seq☆470Updated last week
- Plot structural variant signals from many BAMs and CRAMs☆555Updated last year
- Count bases in BAM/CRAM files☆319Updated 3 years ago
- Tools to process and analyze deep sequencing data.☆741Updated 3 months ago
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆434Updated 2 months ago
- ☆293Updated last month
- This Snakemake pipeline implements the GATK best-practices workflow☆260Updated 2 years ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆454Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆443Updated 10 months ago
- Structural variation caller using third generation sequencing☆622Updated last week
- Tools for working with genomic and high throughput sequencing data.☆348Updated this week
- Haplotype VCF comparison tools☆447Updated last year
- Strelka2 germline and somatic small variant caller☆384Updated 3 years ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆509Updated last week
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆327Updated 5 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆385Updated 2 months ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆527Updated last month
- RNA-seq workflow using STAR and DESeq2☆346Updated last month
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆849Updated 4 months ago
- Customizable workflows based on snakemake and python for the analysis of NGS data☆397Updated last week
- Structural variant and indel caller for mapped sequencing data☆447Updated 2 weeks ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆402Updated 2 months ago
- Data and analysis for NA12878 genome on nanopore☆396Updated 2 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆464Updated 2 months ago
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆492Updated last week
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆535Updated last month
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆275Updated 2 years ago
- Documentation for the ANNOVAR software☆245Updated 3 months ago